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- PDB-29mc: Structure of Anopheles gambiae OBP9 in complex with Methyl eugenol -

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Basic information

Entry
Database: PDB / ID: 29mc
TitleStructure of Anopheles gambiae OBP9 in complex with Methyl eugenol
ComponentsAGAP000278-PA
KeywordsTRANSPORT PROTEIN / Insect Odorant Binding Protein OBP9 Anopheles gambiae Methyl eugenol
Function / homologyInsect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / sensory perception of smell / : / : / Uncharacterized protein
Function and homology information
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsChristodoulou, E. / Stamati, E.C.V. / Tsitsanou, K.E. / Zographos, S.E.
Funding support Greece, European Union, 3items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)HFRI FM17 637 Greece
General Secretariat for Research and Technology (GSRT)MIS 5002550European Union
iNEXT-DiscoveryGA 871037European Union
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Structural insights into ligand recognition by the pleiotropic odorant-binding protein AgamOBP9.
Authors: Christodoulou, E. / Stamati, E.C.V. / Saitta, F. / Papakyriakou, A. / Fessas, D. / Tsitsanou, K.E. / Zographos, S.E.
History
DepositionMar 20, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGAP000278-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4623
Polymers14,0901
Non-polymers3722
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint6 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.686, 43.961, 62.025
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AGAP000278-PA / Odorant-binding protein AgamOBP9


Mass: 14089.935 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: AgamOBP9, 1271980, OBP9, AgaP_AGAP000278 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 (DE3) / References: UniProt: Q8I8R2
#2: Chemical ChemComp-A1J27 / Methyleugenol / 1,2-dimethoxy-4-prop-2-enyl-benzene


Mass: 178.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 28.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 M Ethylene glycols: 0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol 0.1 M Imidazole; MES monohydrate (acid) pH 6.5 30% v/v Mix 1: ...Details: 0.12 M Ethylene glycols: 0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol 0.1 M Imidazole; MES monohydrate (acid) pH 6.5 30% v/v Mix 1: 40% v/v PEG 500* MME; 20% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.88559 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88559 Å / Relative weight: 1
ReflectionResolution: 1.2→62.03 Å / Num. obs: 31058 / % possible obs: 99.4 % / Redundancy: 13 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.022 / Rrim(I) all: 0.076 / Χ2: 1 / Net I/σ(I): 26.4 / Num. measured all: 404856
Reflection shellResolution: 1.2→1.22 Å / % possible obs: 99.8 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.147 / Num. measured all: 21190 / Num. unique obs: 1567 / CC1/2: 0.995 / Rpim(I) all: 0.04 / Rrim(I) all: 0.152 / Χ2: 0.75 / Net I/σ(I) obs: 12.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→35.87 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.985 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18167 1509 4.9 %RANDOM
Rwork0.15361 ---
obs0.15508 29494 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.667 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2---0.17 Å20 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.2→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 26 123 1127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121099
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161041
X-RAY DIFFRACTIONr_angle_refined_deg2.0761.8441490
X-RAY DIFFRACTIONr_angle_other_deg0.7721.8232407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5655140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.61855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73310198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02263
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9981.245513
X-RAY DIFFRACTIONr_mcbond_other3.9731.245513
X-RAY DIFFRACTIONr_mcangle_it5.7712.241647
X-RAY DIFFRACTIONr_mcangle_other5.7712.242648
X-RAY DIFFRACTIONr_scbond_it5.0951.591586
X-RAY DIFFRACTIONr_scbond_other5.0921.594587
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4162.773836
X-RAY DIFFRACTIONr_long_range_B_refined11.50920.081375
X-RAY DIFFRACTIONr_long_range_B_other11.2818.641349
X-RAY DIFFRACTIONr_rigid_bond_restr3.74832140
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 103 -
Rwork0.126 2161 -
obs--98.86 %

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